Table 4

Obtained accuracy of the consensus predictions, in the test set of 20 outer membrane proteins

METHOD

TYPE

SEQUENCE

Qβ

Cβ

SOV

Correctly predicted topologies

Correctly predicted barrel size


PRED-TMBB, ProfTMB, HMM-B2TMR

CONSENSUS

barrel

0.771

0.596

0.877

17

19

precursor

0.818

0.628

0.86

15

18

PRED-TMBB, ProfTMB, HMM-B2TMR, B2TMPRED

CONSENSUS

barrel

0.790

0.616

0.896

17

19

precursor

0.832

0.641

0.865

15

18

PRED-TMBB, ProfTMB, HMM-B2TMR, TBBPred-nn

CONSENSUS

barrel

0.809

0.635

0.917

18

20

precursor

0.839

0.653

0.867

15

18

PRED-TMBB, ProfTMB, HMM-B2TMR, TBBPred-svm

CONSENSUS

barrel

0.809

0.629

0.906

15

19

precursor

0.847

0.658

0.882

15

18

PRED-TMBB, ProfTMB, HMM-B2TMR, TBBPred-comb

CONSENSUS

barrel

0.791

0.607

0.894

17

20

precursor

0.833

0.648

0.859

15

18

PRED-TMBB, ProfTMB, HMM-B2TMR, TBBPred-nn/svm

CONSENSUS

barrel

0.824

0.638

0.92

17

19

precursor

0.85

0.647

0.871

13

17

PRED-TMBB, ProfTMB, HMM-B2TMR, B2TMPRED, TBBPred-nn/svm

CONSENSUS

barrel

0.825

0.637

0.927

17

18

precursor

0.854

0.652

0.876

15

17

PRED-TMBB, ProfTMB, HMM-B2TMR, B2TMPRED, TBBPred-nn

CONSENSUS

barrel

0.819

0.641

0.924

18

20

precursor

0.849

0.660

0.874

15

18

PRED-TMBB, ProfTMB, HMM-B2TMR, B2TMPRED, TBBPred-comb

CONSENSUS

barrel

0.807

0.625

0.907

17

19

precursor

0.845

0.658

0.868

15

18

PRED-TMBB, ProfTMB, HMM-B2TMR, B2TMPRED, TBBPred-svm

CONSENSUS

barrel

0.819

0.637

0.910

15

19

precursor

0.853

0.659

0.880

14

18

PRED-TMBB, ProfTMB, B2TMPRED, TBBPred-svm/nn

CONSENSUS

barrel

0.829

0.642

0.923

17

18

precursor

0.851

0.648

0.861

15

16

PRED-TMBB, ProfTMB, B2TMPRED, TBBPred-svm, TBBPred-nn, HMM-B2TMR, TMBETA-NET, PSI-PRED, BETA-TM

CONSENSUS

barrel

0.808

0.582

0.851

11

13

precursor

0.844

0.604

0.841

12

13


We report the consensus of all the available methods, and the ones that were obtained using the 3 top-scoring HMMs combined in various ways with some of the top-scoring NN/SVM methods. The best results are highlighted with bold. For abbreviations see also Table 1.

Bagos et al. BMC Bioinformatics 2005 6:7   doi:10.1186/1471-2105-6-7

Open Data